rs3803808

Variant names:

• chr17-2049683-G-A
• rs3803808
• XR_007065576.1:n.267C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-2049683-G-A
• chr17-2049683-G-C
• chr17-2049683-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065576.1(LOC124903896):​n.267C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,238 control chromosomes in the GnomAD database, including 990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.060 (990 hom., cov: 32)
• Consequence: LOC124903896 XR_007065576.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 4 publications found

Genes affected

LOC124903896 (HGNC:):

DPH1-AS1 (HGNC:56040): (DPH1 antisense RNA 1)

MIR132 (HGNC:31516): (microRNA 132) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903896	XR_007065576.1	n.267C>T		non_coding_transcript_exon_variant	Exon 1 of 2
MIR132	NR_029674.1	n.*225C>T		downstream_gene_variant
MIR132	unassigned_transcript_2918	n.*246C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPH1-AS1	ENST00000781156.1	n.39-344C>T		intron_variant	Intron 1 of 3
DPH1-AS1	ENST00000781157.1	n.37-344C>T		intron_variant	Intron 1 of 2
DPH1-AS1	ENST00000781158.1	n.183+6C>T		splice_region_variant, intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9125 AN: 152122 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0479

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0600 AC: 9131 AN: 152238 Hom.: 990 Cov.: 32 AF XY: 0.0671 AC XY: 4992 AN XY: 74440

African (AFR) AF: 0.0117 AC: 486 AN: 41558

American (AMR) AF: 0.106 AC: 1616 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2719 AN: 5168

South Asian (SAS) AF: 0.0805 AC: 388 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1073 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2492 AN: 68002

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0455 Hom.: 38

Bravo AF: 0.0580

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.4
DANN	Benign	0.90
PhyloP100		0.091

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3803808; hg19: chr17-1952977;